Dear amber users,
I am trying to perform Random Acceleration Molecular Dynamics (RAMD)simulations
using amber8 in order to explore exit trajectories of a ligand from its docking
position in the buried active site of the enzyme. For this purpose, I would like
to get further information about the time of RAMD simulations and about the
parameter (iramdsd) which is the seed for the random number generator in RAMD
simulations ( default value = 14253). Should I just choose different odd
numbers or odd primes? small or large prime numbers and how large is large
enough to get the best simulation (for example iramds = 100 vs iramdsd = 99999
which the limit of iramdsd variable)
thanks for any advice,
Waad RHAIEM
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Received on Wed Apr 14 2010 - 07:30:03 PDT
